On the design of CRISPR-based single cell molecular screens
Andrew J. Hill,
José L. McFaline-Figueroa,
Lea M. Starita,
Molly J. Gasperini,
Kenneth A. Matreyek,
Posted 29 Jan 2018
bioRxiv DOI: 10.1101/254334 (published DOI: 10.1038/nmeth.4604)
Posted 29 Jan 2018
Several groups recently reported coupling CRISPR/Cas9 perturbations and single cell RNA-seq as a potentially powerful approach for forward genetics. Here we demonstrate that vector designs for such screens that rely on cis linkage of guides and distally located barcodes suffer from swapping of intended guide-barcode associations at rates approaching 50% due to template switching during lentivirus production, greatly reducing sensitivity. We optimize a published strategy, CROP-seq, that instead uses a Pol II transcribed copy of the sgRNA sequence itself, doubling the rate at which guides are assigned to cells to 94%. We confirm this strategy performs robustly and further explore experimental best practices for CRISPR/Cas9-based single cell molecular screens.
- Downloaded 3,620 times
- Download rankings, all-time:
- Site-wide: 1,336 out of 89,671
- In genomics: 290 out of 5,709
- Year to date:
- Site-wide: 10,678 out of 89,671
- Since beginning of last month:
- Site-wide: 13,443 out of 89,671
Downloads over time
Distribution of downloads per paper, site-wide
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!